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Molecular Biology > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

what is the difference between DNA and RNA

A

RNA has a 2’ OH group that allows it to form tertiary structures

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2
Q

what are the purines and how many cyclics do they have

A

adenine, guanine (2)

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3
Q

what are the pyrimidines and how many cyclics do they have

A

cytosine, thymine, uracil (1)

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4
Q

which purine has a double bonded O group on carbon 6

A

guanine

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5
Q

which pyrimidine has a NH2 group on carbon 4

A

cytosine

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6
Q

which C in purines forms the bond with pentose

A

carbon 9

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7
Q

which C in pyrimidines forms the bond with pentose

A

carbon 1

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8
Q

what is the name of the bond that connects the phosphate group to the pentose

A

phosphodiester

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9
Q

what is the name of the bond that connects the pentose to the base (A,T,G,C)

A

glycosidic

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10
Q

describe chargaffs rules

A

number of purines (A+G) = number of pyrimidines (T+C)
the relative ratios between purines and pyrimidines stays constant between different tissues of an individual
DID NOT SAY that T and A pair together and G and C pair together

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11
Q

what base pair combo will result in a higher melting point

A

G-C

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12
Q

what is the difference between ddNTP and dNTP

A

ddNTPs lack a 3’ OH
ddNTPs used to stop
dNTPs used to start

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13
Q

what are ddNTPs used for

A

sanger sequencing

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14
Q

5’ AAC GGT ………….. TAA CTG 3’

what are the primers that should be used for this fragment of DNA

A

left primer 5’ AAC GGT 3’

right primer 5’ CAG TTA 3”

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15
Q

what is the difference between a mutation and a SNP (polymorphism)

A

a mutation is present in less that 1% of the population

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16
Q

what contributes to a 30nm filament

A

histone H1
histone tails
NOT INCLUDED: chromatin remodeling complexes

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17
Q

what are three ways chromatin remodeling complexes modulate gene expression

A

insert, eject, move nucleosomes

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18
Q

what is the light part of a cell called (open)

A

euchromatin

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19
Q

what is the dark part of a cell called (closed)

A

heterochromatin

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20
Q

what is the function of H3.3

A

lock DNA in open confirmation

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21
Q

what is the function of H2A.X

A

recruitment of DNA repair proteins

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22
Q

what is the function of macroH2A.Z

A

inactivation of X chromosome in female cells

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23
Q

what is the function of CENPA

A

binds kinetochores

24
Q

is bromodomain protein associated with open or closed chromatin

A

open

25
Q

is acetylation of histone tails associated with open or closed chromatin

A

open

26
Q

is methylation of histone tails associated with open or closed chromatin

A

closed

27
Q

is high nucleosome density associated with open or closed chromatin

A

closed

28
Q

what does pol III - polymerase domain do

A

performs DNA replication

29
Q

what does helicase do

A

unwinds DNA duplex

30
Q

what does the clamp loader do

A

loads the beta sliding clamp

31
Q

what does primase do

A

synthesizes RNA primer

32
Q

what does topoisomerase do

A

removes topological stress

33
Q

what does pol III 3’ to 5’ exonuclease domain do

A

removes mismatched nucleotides (proofreading) during replication

34
Q

what does the delta subunit of the clamp loader do

A

removes beta clamp after replication

35
Q

what does ligase do

A

catalyzes phosphodiester bond between okazaki fragments (during replication)

36
Q

what remains on the DNA at the end of replication of a okazaki fragment

A

beta sliding clamp

37
Q

what is released from the DNA at the end of replication of a okazaki fragment

A

pol III

38
Q

what enables the removal of the RNA bases and addition of dNTPs on the okazaki fragment after it is replicated

A

pol I 5’ to 3’ exonuclease activity

39
Q

the simultaneous RNA removal and DNA synthesis is called

A

nick translation

40
Q

what is the difference between a PCR and a rtPCR

A

PCR: amplifies DNA sequence
rtPCR: measures amount of DNA

41
Q

1 nucleosome is composed of what histones

A

2x

H2A, H2B, H3, H4

42
Q

1 nucleosome is composed of what histones

A

2x

H2A, H2B, H3, H4

43
Q

how are histones modified

A

specialized histone modifying enzymes

some enzymes add modifications, some remove them

44
Q

is new or old DNA heavier

A

old DNA –> heavier

45
Q

what is the replisome

A

all proteins that work together during DNA replication elongation

46
Q

what is contained in the pol III holoenzyme

A

pol III core, beta sliding clamp, clamp loader

47
Q

what is the role of the pol III core

A

all nucleotides and proofreading

48
Q

what is the role of the beta sliding clamp

A

increase speed of replication

49
Q

what is the role of SSB

A

protects ssDNA

50
Q

what are the initiation steps of replication in bacteria

A
  1. 9mer repeats bound by DnaA
  2. torque destabilizes DNA so DNA opens at 13mer repeats
  3. using the prepriming cortex, replication bubble opens more
  4. primers are made
  5. holoenzyme does replication on both leading strands until it reaches opposite side of bubble
  6. holoenzyme docks
  7. regular replication starts on both strands
51
Q

what is a DAM site

A

GATC, A gets a methyl group added

52
Q

what is it called when on of the two strands is methylated

A

hemimethylated DNA

53
Q

what is the role of seqA

A

seqA recognizes hemimethylated DNA and prevents binding of DnaA –> no replication

54
Q

how is replication regulated so that a second initiation does not occur too early

A

after seqA binds, DAM starts methylation of the new DNA strand; by the time DAM has methylated all of the DAM sites, the entire chromosome is replicated

55
Q

what would happen to replication if DAM was inhibited

A

replication initiation would not happen

56
Q

what are the steps of the cell cycle

A
  1. G1: assembly of the pre-replication complex
  2. S-entry: degradation of preRC
  3. S: assembly of replication complex
57
Q

what happens to replication if cdt1/cdc6 do not remain degraded

A

replication would re-initiate before the previous cycle of replication has finished

Molecular Biology (4 decks)

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